This report is generated by the tcge-cfmedip-seq-pipeline

Selected QC metrics

  • NOTE: The heatmap is drawn based on transformed Z scores. In general, the darker, the worse! Specifically:
    • raw_reads_depth, usable_reads_depth, saturation_maxEstCor and enrichment_GoGe: the darker, the lower
    • coverage_pctReadsWoCpG and coverage_pctCpGwoRead: the darker, the higher
    • fragment_size_mode: the darker, the further away from the mean mode

Reads QC metrics

Summary statistics for raw, prefilter and aligned reads

  • raw_reads_depth: number of raw reads or read pairs
  • prefilter_reads: reads or read pairs after QC, adapter trimming and UMI barcode extraction (p.r.n)
  • mapped_reads_pct: percentage of mapped reads or read pairs over the prefileter_reads
  • usable_reads: reads or read pairs after removing the duplication. reads pairs require properly paired as well
  • usable_reads_pct: percentage of usable reads over raw reads
Number of samples: 161
raw_reads_depth prefilter_reads_depth prefilter_reads_pct prefilter_reads_GC prefilter_reads_dedup_pct mapped_reads_pct usable_reads_depth usable_reads_depth_pct
Min 32262542 32254934 99.95 48.00 18.67 98.29 15034504 19.76
Q1 58117451 58095122 99.97 50.00 46.44 99.68 31244642 50.55
Median 64216388 64194949 99.97 51.00 55.04 99.73 36797783 58.36
Mean 68799904 68781958 99.97 50.94 52.16 99.71 37534977 55.70
Q3 75027262 75001670 99.98 52.00 60.23 99.76 43770337 64.80
Max 165019785 164978205 99.99 57.00 71.05 99.83 96641876 77.71

Usable read depth per sample

Usable read depth percentages against raw read depth per sample

Fragment QC metrics

Fragment size Mode, Mean, Median

Number of samples: 161
fragment_size_mode fragment_size_mean fragment_size_median
Min 165.0 163.0 165.0
Q1 167.0 172.0 170.0
Median 167.0 189.0 175.0
Mean 167.4 192.8 176.3
Q3 168.0 208.0 179.0
Max 177.0 293.0 299.0

Fragment size Mode

Fragment size ranges with >=80% properly paired reads

  • Calculated by based on PICARD MEDIAN_INSERT_SIZE + WIDTH_OF_80_PERCENT/2
    • WIDTH_OF_80_PERCENT: The “width” of the bins, centered around the median, that encompass 80% of all read pairs.

MEDIPS QC metrics

Saturation and Coverage Metrics

Number of samples: 161
saturation_maxEstCor coverage_pctReadsWoCpG coverage_pctCpGwoRead coverage_pctCpGwo1Read coverage_pctCpGgt5Read
Min 0.9900 0.440 20.67 10.60 14.65
Q1 1.0000 0.860 29.77 12.60 27.10
Median 1.0000 1.060 34.41 13.34 32.05
Mean 0.9978 1.185 34.54 13.37 31.20
Q3 1.0000 1.380 38.72 13.96 35.49
Max 1.0000 6.030 51.94 17.82 48.14

Coverage: percentage of usable reads without CpG, and CpGs without reads

Enrichment score per sample